12-54282272-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_031157.4(HNRNPA1):c.462C>T(p.Asp154Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,448 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_031157.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HNRNPA1 | NM_031157.4 | c.462C>T | p.Asp154Asp | synonymous_variant | Exon 4 of 11 | ENST00000340913.11 | NP_112420.1 | |
HNRNPA1 | NM_002136.4 | c.462C>T | p.Asp154Asp | synonymous_variant | Exon 4 of 10 | NP_002127.1 | ||
HNRNPA1 | NR_135167.2 | n.544C>T | non_coding_transcript_exon_variant | Exon 4 of 11 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000681 AC: 17AN: 249744Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135520
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461162Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 726900
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74456
ClinVar
Submissions by phenotype
HNRNPA1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at